Few more questions from a beginner

[J. Cohen]

I've managed to get this far on Lachrimae from the help that people on
the list have provided so far:
http://www.guitarmiami.com/tank/lachrimae.ly
http://www.guitarmiami.com/tank/lachrimae.pdf

I haven't been able to figure out a few things:

* Put some naturals in parentheses (e.g., measures 8 and 9)

* Move rests to correct height.  Many of the rests aren't appearing at
the same height as their voices. (e.g., measures 3 and 7)

* In 4/4 isn't it better to break 8th notes into groups of two instead
of groups of four? (e.g., last measure) Is it possible to do that in
Lilypond?

* Some of the notes are stacked on top of each other. (e.g., measure 4)
 Should I just use padding to move each note individually?